The present invention relates to a plant phenotype, designated PAGODA (PGD), together with DNA and polypeptide sequences associated with the same.
The traditional methods for gene discovery, including chemical mutagenesis, irradiation and T-DNA insertion, used to screen loss of function mutants have limitations. Mutagenic methods such as these rarely identify genes that are redundant in the genome, and gene characterization is time-consuming and laborious.
Activation tagging is a method by which genes are randomly and strongly up-regulated on a genome-wide scale, after which specific phenotypes are screened for and selected. Isolation of mutants by activation tagging has been reported (Hayashi et al., 1992). An activation T-DNA tagging construct was used to activate genes in tobacco cell culture allowing the cells to grow in the absence of plant growth hormones (Walden et al., 1994). Genes have been isolated from plant genomic sequences flanking the T-DNA tag and putatively assigned to plant growth hormone responses. (See, e.g., Miklashevichs et al. 1997, Harling et al., 1997; Walden et. al., 1994; and Schell et al., 1998, which discusses related studies.)
The first gene characterized in Arabidopsis using activation tagging was a gene encoding the histone kinase involved in the cytokinin signal transduction pathway. The gene sequence was isolated from plant genomic DNA by plasmid rescue and the role of the gene, CKI1, in cytokinin responses in plants was confirmed by re-introduction into Arabidopsis (Kakimoto, 1996). This was followed by reports of several dominant mutants such as TINY, LHY and SHI using a similar approach along with the Ds transposable element (Wilson et al., 1996, Schaffer et al., 1998, Fridborg et al., 1999). In a more recent report, activation T-DNA tagging and screening plants for an early flowering phenotype led to the isolation of the FT gene (Kardailsky et al., 1999).
The potential application of activation tagging as a high through put technology for gene discovery has been demonstrated based on screening of several dominant mutant genes involved in photoreceptor, brassinosteroid, gibberellin and flowering signal pathways, as well as disease resistance. (See, e.g., Weigel et al., 2000, Christensen et al., 1998; Kardailsky et al., 1999).
The invention provides nucleic acid and amino acid sequences associated with the PAGODA (xe2x80x9cPGDxe2x80x9d) phenotype in plants, identified for its compact stature, curled leaves, and downward-oriented flowers/siliques relative to wild-type Arabidopsis plants.
In one aspect, the invention provides one or more isolated PGD nucleic acid sequences comprising a nucleic acid sequence that encodes or is complementary to a sequence that encodes a PGD polypeptide having at least 70%, 80%, 90% or more sequence identity to the amino acid sequence presented as SEQ ID NO:2.
In another aspect, the polynucleotide comprises a nucleic acid sequence that hybridizes, under high, medium, or low stringency conditions to the nucleic acid sequence, or fragment thereof, presented as SEQ ID NO:1, or the complement thereof.
In a related aspect, expression of one or more of such PGD polynucleotides in a plant is associated with the PGD phenotype.
The invention further provides plant transformation vectors, plant cells, plant parts and plants comprising a PGD nucleic acid sequence.
Expression of such a PGD nucleic acid sequence in a plant is associated with the PGD phenotype, presented as altered stature and leaf and floral organ morphology relative to the wild type plant.
The expression of a PGD nucleic acid sequence may be modified in ornamental plants, fruit and vegetable-producing plants, grain-producing plants, oil-producing plants and nut-producing plants, as well as other crop plants, resulting in the PGD phenotype.
In a further aspect the invention provides a method of modifying the stature and leaf and floral organ morphology in a plant by introducing a PGD nucleic acid sequence into plant progenitor cells and growing the cells to produce a transgenic plant.
Unless otherwise indicated, all technical and scientific terms used herein have the same meaning as they would to one skilled in the art of the present invention. Practitioners are particularly directed to Sambrook et al., 1989, and Ausubel FM et al., 1993, for definitions and terms of the art. It is to be understood that this invention is not limited to the particular methodology, protocols, and reagents described, as these may vary.
All publications cited herein, and listed below immediately after the examples, are expressly incorporated herein by reference for the purpose of describing and disclosing compositions and methodologies that might be used in connection with the invention.
As used herein, the term xe2x80x9cvectorxe2x80x9d refers to a nucleic acid construct designed for transfer between different host cells. An xe2x80x9cexpression vectorxe2x80x9d refers to a vector that has the ability to incorporate and express heterologous DNA fragments in a foreign cell. Many prokaryotic and eukaryotic expression vectors are commercially available. Selection of appropriate expression vectors is within the knowledge of those having skill in the art.
A xe2x80x9cheterologousxe2x80x9d nucleic acid construct or sequence has a portion of the sequence which is not native to the plant cell in which it is expressed. Heterologous, with respect to a control sequence refers to a control sequence (i.e. promoter or enhancer) that does not function in nature to regulate the same gene the expression of which it is currently regulating. Generally, heterologous nucleic acid sequences are not endogenous to the cell or part of the genome in which they are present, and have been added to the cell, by infection, transfection, microinjection, electroporation, or the like. A xe2x80x9cheterologousxe2x80x9d nucleic acid construct may contain a control sequence/DNA coding sequence combination that is the same as, or different from a control sequence/DNA coding sequence combination found in the native plant.
As used herein, the term xe2x80x9cgenexe2x80x9d means the segment of DNA involved in producing a polypeptide chain, which may or may not include regions preceding and following the coding region, e.g. 5 xe2x80x2 untranslated (5xe2x80x2 UTR) or xe2x80x9cleaderxe2x80x9d sequences and 3xe2x80x2 UTR or xe2x80x9ctrailerxe2x80x9d sequences, as well as intervening sequences (introns) between individual coding segments (exons).
As used herein, xe2x80x9cpercent (%) sequence identityxe2x80x9d with respect to a subject sequence, or a specified portion of a subject sequence, is defined as the percentage of nucleotides or amino acids in the candidate derivative sequence identical with the nucleotides or amino acids in the subject sequence (or specified portion thereof), after aligning the sequences and introducing gaps, if necessary to achieve the maximum percent sequence identity, as generated by the program WU-BLAST-2.0al9 (Altschul et al., J. Mol. Biol. (1997) 215:403-410; blast.wustl.edu/blast/README.html website) with all the search parameters set to default values. The HSP S and HSP S2 parameters are dynamic values and are established by the program itself depending upon the composition of the particular sequence and composition of the particular database against which the sequence of interest is being searched. A % identity value is determined by the number of matching identical nucleotides or amino acids divided by the sequence length for which the percent identity is being reported. xe2x80x9cPercent (%) amino acid sequence similarityxe2x80x9d is determined by doing the same calculation as for determining % amino acid sequence identity, but including conservative amino acid substitutions in addition to identical amino acids in the computation.
The term xe2x80x9c% homologyxe2x80x9d is used interchangeably herein with the term xe2x80x9c% identity.xe2x80x9d
A nucleic acid sequence is considered to be xe2x80x9cselectively hybridizablexe2x80x9d to a reference nucleic acid sequence if the two sequences specifically hybridize to one another under moderate to high stringency hybridization and wash conditions. Hybridization conditions are based on the melting temperature (Tm) of the nucleic acid binding complex or probe. For example, xe2x80x9cmaximum stringencyxe2x80x9d typically occurs at about Tm-5xc2x0 C. (5xc2x0 below the Tm of the probe); xe2x80x9chigh stringencyxe2x80x9d at about 5-10xc2x0 below the Tm; xe2x80x9cintermediate stringencyxe2x80x9d at about 10-20xc2x0 below the Tm of the probe; and xe2x80x9clow stringencyxe2x80x9d at about 20-25xc2x0 below the Tm. Functionally, maximum stringency conditions may be used to identify sequences having strict identity or near-strict identity with the hybridization probe; while high stringency conditions are used to identify sequences having about 80% or more sequence identity with the probe.
Moderate and high stringency hybridization conditions are well known in the art (see, for example, Sambrook, et al, 1989, Chapters 9 and 11, and in Ausubel, F. M., et al., 1993, expressly incorporated by reference herein). An example of high stringency conditions includes hybridization at about 42xc2x0 C. in 50% formamide, 5xc3x97SSC, 5xc3x97Denhardt""s solution, 0.5% SDS and 100 xcexcg/ml denatured carrier DNA followed by washing two times in 2xc3x97SSC and 0.5% SDS at room temperature and two additional times in 0.1xc3x97SSC and 0.5% SDS at 42xc2x0 C.
As used herein, xe2x80x9crecombinantxe2x80x9d includes reference to a cell or vector, that has been modified by the introduction of a heterologous nucleic acid sequence or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found in identical form within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all as a result of deliberate human intervention.
As used herein, the terms xe2x80x9ctransformedxe2x80x9d, xe2x80x9cstably transformedxe2x80x9d or xe2x80x9ctransgenicxe2x80x9d with reference to a plant cell means the plant cell has a non-native (heterologous) nucleic acid sequence integrated into its genome which is maintained through two or more generations.
As used herein, the term xe2x80x9cexpressionxe2x80x9d refers to the process by which a polypeptide is produced based on the nucleic acid sequence of a gene. The process includes both transcription and translation.
The term xe2x80x9cintroducedxe2x80x9d in the context of inserting a nucleic acid sequence into a cell, means xe2x80x9ctransfectionxe2x80x9d, or xe2x80x9ctransformationxe2x80x9d or xe2x80x9ctransductionxe2x80x9d and includes reference to the incorporation of a nucleic acid sequence into a eukaryotic or prokaryotic cell where the nucleic acid sequence may be incorporated into the genome of the cell (for example, chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (for example, transfected mRNA).
As used herein, a xe2x80x9cplant cellxe2x80x9d refers to any cell derived from a plant, including cells from undifferentiated tissue (e.g., callus) as well as plant seeds, pollen, progagules and embryos.
As used herein, the terms xe2x80x9cnativexe2x80x9d and xe2x80x9cwild-typexe2x80x9d relative to a given plant trait or phenotype refers to the form in which that trait or phenotype is found in the same variety of plant in nature.
As used herein, the term xe2x80x9cmodifiedxe2x80x9d regarding a plant trait, refers to a change in the phenotype of a transgenic plant relative to a non-transgenic plant, as it is found in nature.
As used herein, the term xe2x80x9cT1xe2x80x9d refers to the generation of plants from the seed of T0 plants. The T1 generation is the first set of transformed plants that can be selected by application of a selection agent, e.g., an antibiotic or herbicide, for which the transgenic plant contains the corresponding resistance gene.
As used herein, the term xe2x80x9cT2xe2x80x9d refers to the generation of plants by self-fertilization of the flowers of T1 plants, previously selected as being transgenic.
As used herein, the term xe2x80x9cplant partxe2x80x9d includes any plant organ or tissue including, without limitation, seeds, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, and microspores. Plant cells can be obtained from any plant organ or tissue and cultures prepared therefrom. The class of plants which can be used in the methods of the present invention is generally as broad as the class of higher plants amenable to transformation techniques, including both monocotyledenous and dicotyledenous plants.
As used herein, xe2x80x9ctransgenic plantxe2x80x9d includes reference to a plant that comprises within its genome a heterologous polynucleotide. Generally, the heterologous polynucleotide is stably integrated within the genome such that the polynucleotide is passed on to successive generations. The heterologous polynucleotide may be integrated into the genome alone or as part of a recombinant expression cassette. xe2x80x9cTransgenicxe2x80x9d is used herein to include any cell, cell line, callus, tissue, plant part or plant, the genotype of which has been altered by the presence of heterologous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic.
Thus a plant having within its cells a heterologous polynucleotide is referred to herein as a xe2x80x9ctransgenic plantxe2x80x9d. The heterologous polynucleotide can be either stably integrated into the genome, or can be extra-chromosomal. Preferably, the polynucleotide of the present invention is stably integrated into the genome such that the polynucleotide is passed on to successive generations. The polynucleotide is integrated into the genome alone or as part of a recombinant expression cassette. xe2x80x9cTransgenicxe2x80x9d is used herein to include any cell, cell line, callus, tissue, plant part or plant, the genotype of which has been altered by the presence of heterologous nucleic acids including those transgenics initially so altered as well as those created by sexual crosses or asexual reproduction of the initial transgenics.
A plant cell, tissue, organ, or plant into which the recombinant DNA constructs containing the expression constructs have been introduced is considered xe2x80x9ctransformedxe2x80x9d, xe2x80x9ctransfectedxe2x80x9d, or xe2x80x9ctransgenicxe2x80x9d. A transgenic or transformed cell or plant also includes progeny of the cell or plant and progeny produced from a breeding program employing such a transgenic plant as a parent in a cross and exhibiting an altered phenotype resulting from the presence of a recombinant nucleic acid sequence. Hence, a plant of the invention will include any plant which has a cell containing a construct with introduced nucleic acid sequences, regardless of whether the sequence was introduced into the directly through transformation means or introduced by generational transfer from a progenitor cell which originally received the construct by direct transformation.
The terms xe2x80x9cPAGODAxe2x80x9d and xe2x80x9cPGDxe2x80x9d, as used herein encompass native PAGODA (PGD) nucleic acid and amino acid sequences, homologues, variants and fragments thereof.
An xe2x80x9cisolatedxe2x80x9d PGD nucleic acid molecule is a PGD nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the PGD nucleic acid. An isolated PGD nucleic acid molecule is other than in the form or setting in which it is found in nature. However, an isolated PGD nucleic acid molecule includes PGD nucleic acid molecules contained in cells that ordinarily express PGD where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
As used herein, the term xe2x80x9cmutantxe2x80x9d with reference to a polynucleotide sequence or gene differs from the corresponding wild type polynucleotide sequence or gene either in terms of sequence or expression, where the difference contributes to a modified plant phenotype or trait. Relative to a plant or plant line, the term xe2x80x9cmutantxe2x80x9d refers to a plant or plant line which has a modified plant phenotype or trait, where the modified phenotype or trait is associated with the modified expression of a wild type polynucleotide sequence or gene.
Generally, a xe2x80x9cvariantxe2x80x9d polynucleotide sequence encodes a xe2x80x9cvariantxe2x80x9d amino acid sequence which is altered by one or more amino acids from the reference polypeptide sequence. The variant polynucleotide sequence may encode a variant amino acid sequence having xe2x80x9cconservativexe2x80x9d or xe2x80x9cnon-conservativexe2x80x9d substitutions. Variant polynucleotides may also encode variant amino acid sequences having amino acid insertions or deletions, or both.
As used herein, the term xe2x80x9cphenotypexe2x80x9d may be used interchangeably with the term xe2x80x9ctraitxe2x80x9d. The terms refer to a plant characteristic which is readily observable or measurable and results from the interaction of the genetic make-up of the plant with the environment in which it develops. Such a phenotype includes chemical changes in the plant make-up resulting from enhanced gene expression which may or may not result in morphological changes in the plant, but which are measurable using analytical techniques known to those of skill in the art.
As used herein, the term xe2x80x9cinteresting phenotypexe2x80x9d with reference to a plant produced by the methods described herein refers to a readily observable or measurable phenotype demonstrated by a T1 and/or subsequent generation plant, which is not displayed by a plant that has not been so transformed (and/or is not the progeny of a plant that has been so transformed) and represents an improvement in the plant. An xe2x80x9cimprovementxe2x80x9d is a feature that may enhance the utility of a plant species or variety by providing the plant with a unique quality. By unique quality is meant a novel feature or a change to an existing feature of the plant species which is a quantitative change (increase or decrease) or a qualitative change in a given feature or trait.
The gene and phenotype of this invention were identified in a large-scale screen using activation tagging. Activation tagging is a process by which a heterologous nucleic acid construct comprising a nucleic acid control sequence, e.g. an enhancer, is inserted into a plant genome. The enhancer sequences act to enhance transcription of a one or more native plant genes (See, e.g., Walden R, et al., 1994; Weigel D et al. 2000).
Briefly, a large number of Arabidopsis plants were transformed with the activation tagging vector pSKI015 (Weigel et al, 2000), which comprises a T-DNA (i.e., the sequence derived from the Ti plasmid of Agrobacterium tumifaciens that are transferred to a plant cell host during Agrobacterium infection), an enhancer element and a selectable marker gene. Following random insertion of pSKI015 into the genome of transformed plants, the enhancer element can result in up-regulation genes in the vicinity of the T-DNA insertion, generally within 5-10 kilobase (kb) of the insertion. In the T1 generation, plants were exposed to the selective agent in order to specifically recover those plants that expressed the selectable marker and therefore harbored insertions of the activation-tagging vector. Transformed plants were observed for interesting phenotypes, which are generally identified at the T1, T2 and/or T3 generations. Interesting phenotypes may be identified based on morphology, a biochemical screen, herbicide tolerance testing, herbicide target identification, fungal or bacterial resistance testing, insect or nematode resistance testing, screening for stress tolerance, such as drought, salt or antibiotic tolerance, and output traits, such as oil, starch, pigment, or vitamin composition. Genomic sequence surrounding the T-DNA insertion is analyzed in order to identify genes responsible for the interesting phenotypes. Genes responsible for causing such phenotypes are identified as attractive targets for manipulation for agriculture, food, ornamental plant, and/or pharmaceutical industries.
It will be appreciated that in most cases when a modified phenotype results from the enhanced expression of a tagged gene, the phenotype is dominant. In some cases, the enhanced expression of a given native plant gene or a fragment thereof may result in decreased expression or inactivation of its homologue or another native plant gene, which results in the interesting phenotype. The T-DNA insertion may also result in disruption (xe2x80x9closs-of-functionxe2x80x9d) of a native plant gene, in which case the phenotype is generally recessive.
The present invention provides a morphological phenotype, identified in Arabidopsis where T1, T2, and T3 plants were observed as having a compact stature with curled leaves and downward-oriented (xe2x80x9cbrevi-pedicelxe2x80x9d or xe2x80x9cbasi-petalxe2x80x9d) flowers/siliques, which is referred to as the PGD phenotype.
The invention also provides a newly identified and isolated nucleic acid sequence that was identified by analysis of the genomic DNA sequence surrounding the T-DNA insertion correlating with the PGD phenotype. In particular, applicants have identified and characterized the open reading frame of the PGD gene, which is specifically overexpressed in plants having the PGD phenotype, and which is provided in SEQ ID NO:1. A detailed description of the isolation and characterization of PGD is set forth in the Examples.
The PGD gene may be used in the development of transgenic plants having a desired phenotype. This may be accomplished using the native PGD sequence, a variant PGD sequence or a homologue or fragment thereof.
A PGD nucleic acid sequence of this invention may be a DNA or RNA sequence, derived from genomic DNA, cDNA or mRNA. The nucleic acid sequence may be cloned, for example, by isolating genomic DNA from an appropriate source, and amplifying and cloning the sequence of interest using PCR. Alternatively, nucleic acid sequence may be synthesized, either completely or in part, especially where it is desirable to provide plant-preferred sequences. Thus, all or a portion of the desired structural gene (that portion of the gene which encodes a polypeptide or protein) may be synthesized using codons preferred by a selected host.
The invention provides a polynucleotide comprising a nucleic acid sequence which encodes or is complementary to a sequence which encodes a PGD polypeptide having the amino acid sequence presented in SEQ ID NO:2 and a polynucleotide sequence identical over its entire length to the PGD nucleic acid sequence presented SEQ ID NO:1. The invention also provides the coding sequence for the mature PGD polypeptide, a variant or fragment thereof, as well as the coding sequence for the mature polypeptide or a fragment thereof in a reading frame with other coding sequences, such as those encoding a leader or secretory sequence, a pre-, pro-, or prepro- protein sequence.
A PGD polynucleotide can also include non-coding sequences, including for example, but not limited to, non-coding 5xe2x80x2 and 3xe2x80x2 sequences, such as the transcribed, untranslated sequences, termination signals, ribosome binding sites, sequences that stabilize mRNA, introns, polyadenylation signals, and additional coding sequence that encodes additional amino acids. For example, a marker sequence can be included to facilitate the purification of the fused polypeptide. Polynucleotides of the present invention also include polynucleotides comprising a structural gene and the naturally associated sequences that control gene expression.
When an isolated polynucleotide of the invention comprises a PGD nucleic acid sequence flanked by non-PGD nucleic acid sequence, the total length of the combined polynucleotide is typically less than 25 kb, and usually less than 20 kb, or 15 kb, and in some cases less than 10 kb, or 5 kb.
In addition to the PGD nucleic acid and corresponding polypeptide sequences described herein, it is contemplated that PGD variants can be prepared. PGD variants can be prepared by introducing appropriate nucleotide changes into the PGD nucleic acid sequence; by synthesis of the desired PGD polypeptide or by altering the expression level of the PGD gene in plants. Those skilled in the art will appreciate that amino acid changes may alter post-translational processing of the PGD polypeptide, such as changing the number or position of glycosylation sites or altering the membrane anchoring characteristics.
In one aspect, preferred PGD coding sequences include a polynucleotide comprising a nucleic acid sequence which encodes or is complementary to a sequence which encodes a PGD polypeptide having at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more sequence identity to the amino acid sequence presented in SEQ ID NO:2.
In another aspect, preferred variants include a PGD polynucleotide sequence that is at least 50% to 60% identical over its entire length to the PGD nucleic acid sequence presented as SEQ ID NO:1, and nucleic acid sequences that are complementary to such a PGD sequence. More preferable are PGD polynucleotide sequences comprise a region having at least 70%, 80%, 85%, 90% or 95% or more sequence identity to the PGD sequence presented as SEQ ID NO:1.
In a related aspect, preferred variants include polynucleotides that are be xe2x80x9cselectively hybridizablexe2x80x9d to the PGD polynucleotide sequence presented as SEQ ID NO:1.
Sequence variants also include nucleic acid molecules that encode the same polypeptide as encoded by the PGD polynucleotide sequence described herein. Thus, where the coding frame of an identified nucleic acid molecules is known, for example by homology to known genes or by extension of the sequence, it is appreciated that as a result of the degeneracy of the genetic code, a number of coding sequences can be produced. For example, the triplet CGT encodes the amino acid arginine. Arginine is alternatively encoded by CGA, CGC, CGG, AGA, and AGG. Therefore it is appreciated that such substitutions in the coding region fall within the sequence variants that are covered by the present invention. Any and all of these sequence variants can be utilized in the same way as described herein for the identified PGD parent sequence, SEQ ID NO:1.
It is further appreciated that such sequence variants may or may not selectively hybridize to the parent sequence. This would be possible, for example, when the sequence variant includes a different codon for each of the amino acids encoded by the parent nucleotide. Such variants are, nonetheless, specifically contemplated and encompassed by the present invention. In accordance with the present invention, also encompassed are sequences that at least 70% identical to such degeneracy-derived sequence variants.
Although PGD nucleotide sequence variants are preferably capable of hybridizing to the nucleotide sequences recited herein under conditions of moderately high or high stringency, there are, in some situations, advantages to using variants based on the degeneracy of the code, as described above. For example, codons may be selected to increase the rate at which expression of the peptide occurs in a particular prokaryotic or eukaryotic organism, in accordance with the optimum codon usage dictated by the particular host organism. Alternatively, it may be desirable to produce RNA having longer half lives than the mRNA produced by the recited sequences.
Variations in the native full-length PGD nucleic acid sequence described herein, may be made, for example, using any of the techniques and guidelines for conservative and non-conservative mutations, as generally known in the art, oligonucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis (Kunkel T A et al., 1991); cassette mutagenesis (Crameri A et al., 1995); restriction selection mutagenesis (Haught C et al., 1994), or other known techniques can be performed on the cloned DNA to produce nucleic acid sequences encoding PGD variants.
It is contemplated that the gene sequences associated with the PGD phenotype may be synthesized, either completely or in part, especially where it is desirable to provide host-preferred sequences. Thus, all or a portion of the desired structural gene (that portion of the gene which encodes the protein) may be synthesized using codons preferred by a selected host. Host-preferred codons may be determined, for example, from the codons used most frequently in the proteins expressed in a desired host species.
It is preferred that a PGD polynucleotide encodes a PGD polypeptide that retains substantially the same biological function or activity as the mature PGD polypeptide encoded by the polynucleotide set forth as SEQ ID NO:1 (i.e. results in a PGD phenotype when overexpressed in a plant).
Variants also include fragments of the PGD polynucleotide of the invention, which can be used to synthesize a full-length PGD polynucleotide. Preferred embodiments include polynucleotides encoding polypeptide variants wherein 5 to 10, 1 to 5, 1 to 3, 2, 1 or no amino acid residues of a PGD polypeptide sequence of the invention are substituted, added or deleted, in any combination. Particularly preferred are substitutions, additions, and deletions that are silent such that they do not alter the properties or activities of the polynucleotide or polypeptide.
A nucleotide sequence encoding a PGD polypeptide can also be used to construct hybridization probes for further genetic analysis. Screening of a cDNA or genomic library with the selected probe may be conducted using standard procedures, such as described in Sambrook et al., 1989). Hybridization conditions, including moderate stringency and high stringency, are provided in Sambrook et al., supra.
The probes or portions thereof may also be employed in PCR techniques to generate a pool of sequences for identification of closely related PGD sequences. When PGD sequences are intended for use as probes, a particular portion of a PGD encoding sequence, for example a highly conserved portion of the coding sequence may be used.
For example, a PGD nucleotide sequence may be used as a hybridization probe for a cDNA library to isolate genes, for example, those encoding naturally-occurring variants of PGD from other plant species, which have a desired level of sequence identity to the PGD nucleotide sequence disclosed in SEQ ID NO:1. Exemplary probes have a length of about 20 to about 50 bases.
In another exemplary approach, a nucleic acid encoding a PGD polypeptide may be obtained by screening selected cDNA or genomic libraries using the deduced amino acid sequence disclosed herein, and, if necessary, using conventional primer extension procedures as described in Sambrook et al., supra, to detect PGD precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA.
As discussed above, nucleic acid sequences of this invention may include genomic, cDNA or mRNA sequence. By xe2x80x9cencodingxe2x80x9d is meant that the sequence corresponds to a particular amino acid sequence either in a sense or anti-sense orientation. By xe2x80x9cextrachromosomalxe2x80x9d is meant that the sequence is outside of the plant genome of which it is naturally associated. By xe2x80x9crecombinantxe2x80x9d is meant that the sequence contains a genetically engineered modification through manipulation via mutagenesis, restriction enzymes, and the like.
Once the desired form of a PGD nucleic acid sequence, homologue, variant or fragment thereof, is obtained, it may be modified in a variety of ways. Where the sequence involves non-coding flanking regions, the flanking regions may be subjected to resection, mutagenesis, etc. Thus, transitions, transversions, deletions, and insertions may be performed on the naturally occurring sequence.
With or without such modification, the desired form of the PGD nucleic acid sequence, homologue, variant or fragment thereof, may be incorporated into a plant expression vector for transformation of plant cells.
In one preferred embodiment, the invention provides a PGD polypeptide, having a native mature or full-length PGD polypeptide sequence comprising the sequence presented in SEQ ID NO:2. A PGD polypeptide of the invention can be the mature PGD polypeptide, part of a fusion protein or a fragment or variant of the PGD polypeptide sequence presented in SEQ ID NO:2.
Ordinarily, a PGD polypeptide of the invention has at least 50% to 60% identity to a PGD amino acid sequence over its entire length. More preferable are PGD polypeptide sequences that comprise a region having at least 70%, 80%, 85%, 90% or 95% or more sequence identity to the PGD polypeptide sequence of SEQ ID NO:2.
Fragments and variants of the PGD polypeptide sequence of SEQ ID NO:2, are also considered to be a part of the invention. A fragment is a variant polypeptide that has an amino acid sequence that is entirely the same as part but not all of the amino acid sequence of the previously described polypeptides. Exemplary fragments comprises at least 10, 20, 30, 40, 50, 75, or 100 contiguous amino acids of SEQ ID NO:2. The fragments can be xe2x80x9cfree-standingxe2x80x9d or comprised within a larger polypeptide of which the fragment forms a part or a region, most preferably as a single continuous region. Preferred fragments are biologically active fragments, which are those fragments that mediate activities of the polypeptides of the invention, including those with similar activity or improved activity or with a decreased activity. Also included are those fragments that antigenic or immunogenic in an animal, particularly a human.
PGD polypeptides of the invention also include polypeptides that vary from the PGD polypeptide sequence of SEQ ID NO:2. These variants may be substitutional, insertional or deletional variants. The variants typically exhibit the same qualitative biological activity as the naturally occurring analogue, although variants can also be selected which have modified characteristics as further described below.
A xe2x80x9csubstitutionxe2x80x9d results from the replacement of one or more nucleotides or amino acids by different nucleotides or amino acids, respectively.
An xe2x80x9cinsertionxe2x80x9d or xe2x80x9cadditionxe2x80x9d is that change in a nucleotide or amino acid sequence which has resulted in the addition of one or more nucleotides or amino acid residues, respectively, as compared to the naturally occurring sequence.
A xe2x80x9cdeletionxe2x80x9d is defined as a change in either nucleotide or amino acid sequence in which one or more nucleotides or amino acid residues, respectively, are absent.
Amino acid substitutions are typically of single residues; insertions usually will be on the order of from about 1 to 20 amino acids, although considerably larger insertions may be tolerated. Deletions range from about 1 to about 20 residues, although in some cases deletions may be much larger.
Substitutions, deletions, insertions or any combination thereof may be used to arrive at a final derivative. Generally these changes are done on a few amino acids to minimize the alteration of the molecule. However, larger changes may be tolerated in certain circumstances.
Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements. Insertions or deletions may optionally be in the range of 1 to 5 amino acids.
Substitutions are generally made in accordance with known xe2x80x9cconservative substitutionsxe2x80x9d. A xe2x80x9cconservative substitutionxe2x80x9d refers to the substitution of an amino acid in one class by an amino acid in the same class, where a class is defined by common physicochemical amino acid side chain properties and high substitution frequencies in homologous proteins found in nature (as determined, e.g., by a standard Dayhoff frequency exchange matrix or BLOSUM matrix). (See generally, Doolittle, R. F., 1986.)
A xe2x80x9cnon-conservative substitutionxe2x80x9d refers to the substitution of an amino acid in one class with an amino acid from another class.
PGD polypeptide variants typically exhibit the same qualitative biological activity as the naturally occurring analogue, although variants also are selected to modify the characteristics of the PGD polypeptide, as needed. For example, glycosylation sites, and more particularly one or more O-linked or N-linked glycosylation sites may be altered or removed. Those skilled in the art will appreciate that amino acid changes may alter post-translational processes of the PGD polypeptide, such as changing the number or position of glycosylation sites or altering the membrane anchoring characteristics.
The variations can be made using methods known in the art such as oligonucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis [Carter et al., 1986; Zoller et al., 1987], cassette mutagenesis [Wells et al., 1985], restriction selection mutagenesis [Wells et al., 1986] or other known techniques can be performed on the cloned DNA to produce the PGD polypeptide-encoding variant DNA.
Also included within the definition of PGD polypeptides are other related PGD polypeptides. Thus, probe or degenerate PCR primer sequences may be used to find other related polypeptides. Useful probe or primer sequences may be designed to all or part of the PGD polypeptide sequence, or to sequences outside the coding region. As is generally known in the art, preferred PCR primers are from about 15 to about 35 nucleotides in length, with from about 20 to about 30 being preferred, and may contain inosine as needed. The conditions for the PCR reaction are generally known in the art.
Covalent modifications of PGD polypeptides are also included within the scope of this invention. For example, the invention provides PGD polypeptides that are a mature protein and may comprise additional amino or carboxyl-terminal amino acids, or amino acids within the mature polypeptide (for example, when the mature form of the protein has more than one polypeptide chain). Such sequences can, for example, play a role in the processing of a protein from a precursor to a mature form, allow protein transport, shorten or lengthen protein half-life, or facilitate manipulation of the protein in assays or production. It is contemplated that cellular enzymes can be used to remove any additional amino acids from the mature protein. [See, e.g., Creighton, T E, 1983].
In a preferred embodiment, overexpression of a PGD polypeptide or variant thereof is associated with the PGD phenotype.
The present invention further provides anti-PGD polypeptide antibodies. The antibodies may be polyclonal, monoclonal, humanized, bispecific or heteroconjugate antibodies.
Methods of preparing polyclonal antibodies are known to the skilled artisan. Such polyclonal antibodies can be produced in a mammal, for example, following one or more injections of an immunizing agent, and preferably, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected into the mammal by a series of subcutaneous or intraperitoneal injections. The immunizing agent may include a PGD polypeptide or a fusion protein thereof. It may be useful to conjugate the antigen to a protein known to be immunogenic in the mammal being immunized. The immunization protocol may be determined by one skilled in the art based on standard protocols or by routine experimentation.
Alternatively, the anti-PGD polypeptide antibodies may be monoclonal antibodies. Monoclonal antibodies may be produced by hybridomas, wherein a mouse, hamster, or other appropriate host animal, is immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent [Kohler et al., 1975]. Monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567.
The anti-PGD polypeptide antibodies of the invention may further comprise humanized antibodies or human antibodies. The term xe2x80x9chumanized antibodyxe2x80x9d refers to humanized forms of non-human (e.g., murine) antibodies that are chimeric antibodies, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fabxe2x80x2, F(abxe2x80x2)2 or other antigen-binding partial sequences of antibodies) which contain some portion of the sequence derived from non-human antibody. Methods for humanizing non-human antibodies are well known in the art, as further detailed in Jones et al., 1986; Riechmann et al., 1988; and Verhoeyen et al., 1988. Methods for producing human antibodies are also known in the art. See, e.g., Jakobovits, A, et al., 1995; Jakobovits, A, 1995.
In one exemplary approach, anti-PGD polyclonal antibodies are used for gene isolation. Western blot analysis may be conducted to determine that PGD or a related protein is present in a crude extract of a particular plant species. When reactivity is observed, genes encoding the related protein may be isolated by screening expression libraries representing the particular plant species. Expression libraries can be constructed in a variety of commercially available vectors, including lambda gtl 1, as described in Sambrook, et al. , 1989.
From the foregoing, it can be appreciated that the PGD nucleotide sequence, protein sequence and phenotype find utility in modulated expression of the PGD protein and the development of non-native phenotypes associated with such modulated expression.
The PGD phenotype has features that distinguish the mutant from wild type Arabidopsis. The invention has application to ornamental plants and in the cut flower industry. For example, the phenotype could be applied to the well-known garden plants such as the wallflower (Cherianthus cheiri), Honesty and Aubretia of the Cruciferae family and to ornamental tobacco (Nicotiana alata) a solanaceous member and other ornamental plant species. The degree of stem and inflorescence bending is one of the parameters of cut flower quality (Jong, J. de et al., Acta Horticulturae, 482: 287-290, 1999; Littlejohn and Blomerus, Genetic Resources and Crop Protection 44: 227-234, 1997).
In addition, the modulated expression of PGD could be used to change the branching architecture of trees that could have an impact on wood processing industry. In addition, the appressed pod (silique) feature could be applied to certain legumes for efficient pod set, prevention of early shattering of pods and may facilitate harvest, e.g., of Canola.
The observed morphology is one version of the phenotype. The expression of the PGD gene may be modulated with regard to the level of expression and also the tissue specificity of expression. For example: the pendulous trait could be expressed in the leaves at a desired angle so as to increase the photoreception area leading to increased photosynthate production. Such a modification is applicable to herbaceous crops/major cereal crops/legumes/trees.
In practicing the invention, the PGD phenotype and modified PGD expression is generally applicable to any type of plant
The methods described herein are generally applicable to all plants. Although activation tagging and gene identification is carried out in Arabidopsis, following identification of a nucleic acid sequence and associated phenotype, the selected gene, a homologue, variant or fragment thereof, may be expressed in any type of plant. In one aspect, the invention is directed to fruit- and vegetable-bearing plants. In a related aspect, the invention is directed to the cut flower industry, grain-producing plants, oil-producing plants and nut-producing plants, as well as other crops including, but not limited to, cotton (Gossypium), alfalfa (Medicago sativa), flax (Linum usitatissimum), tobacco (Nicotiana), turfgrass (Poaceae family), and other forage crops.
The skilled artisan will recognize that a wide variety of transformation techniques exist in the art, and new techniques are continually becoming available. Any technique that is suitable for the target host plant can be employed within the scope of the present invention. For example, the constructs can be introduced in a variety of forms including, but not limited to as a strand of DNA, in a plasmid, or in an artificial chromosome. The introduction of the constructs into the target plant cells can be accomplished by a variety of techniques, including, but not limited to Agrobacterium-mediated transformation, electroporation, microinjection, microprojectile bombardment calcium-phosphate-DNA co-precipitation or liposome-mediated transformation of a heterologous nucleic acid construct comprising the PGD coding sequence. The transformation of the plant is preferably permanent, i.e. by integration of the introduced expression constructs into the host plant genome, so that the introduced constructs are passed onto successive plant generations.
In one embodiment, binary Ti-based vector systems may be used to transfer and confirm the association between enhanced expression of an identified gene with a particular plant trait or phenotype. Standard Agrobacterium binary vectors are known to those of skill in the art and many are commercially available, such as pBI121 (Clontech Laboratories, Palo Alto, Calif.).
The optimal procedure for transformation of plants with Agrobacterium vectors will vary with the type of plant being transformed. Exemplary methods for Agrobacterium-mediated transformation include transformation of explants of hypocotyl, shoot tip, stem or leaf tissue, derived from sterile seedlings and/or plantlets. Such transformed plants may be reproduced sexually, or by cell or tissue culture. Agrobacterium transformation has been previously described for a large number of different types of plants and methods for such transformation may be found in the scientific literature.
Depending upon the intended use, a heterologous nucleic acid construct may be made which comprises a nucleic acid sequence associated with the PGD phenotype, and which encodes the entire protein, or a biologically active portion thereof for transformation of plant cells and generation of transgenic plants.
The expression of a PGD nucleic acid sequence or a homologue, variant or fragment thereof may be carried out under the control of a constitutive, inducible or regulatable promoter. In some cases expression of the PGD nucleic acid sequence or homologue, variant or fragment thereof may regulated in a developmental stage or tissue-associated or tissue-specific manner. Accordingly, expression of the nucleic acid coding sequences described herein may be regulated with respect to the level of expression, the tissue type(s) where expression takes place and/or developmental stage of expression leading to a wide spectrum of applications wherein the expression of a PGD coding sequence is modulated in a plant.
Strong promoters with enhancers may result in a high level of expression. When a low level of basal activity is desired, a weak promoter may be a better choice. Expression of PGD nucleic acid sequence or homologue, variant or fragment thereof may also be controlled at the level of transcription, by the use of cell type specific promoters or promoter elements in the plant expression vector.
Numerous promoters useful for heterologous gene expression are available. Exemplary constitutive promoters include the raspberry E4 promoter (U.S. Pat. Nos. 5,783,393 and 5,783,394), the 35S CaMV (Jones J D et al, 1992), the CsVMV promoter (Verdaguer B et al., 1998) and the melon actin promoter. Exemplary tissue-specific promoters include the tomato E4 and E8 promoters (U.S. Pat. No. 5,859,330) and the tomato 2AII gene promoter (Van Haaren M J J et al., 1993).
When PGD sequences are intended for use as probes, a particular portion of a PGD encoding sequence, for example a highly conserved portion of a coding sequence may be used.
In yet another aspect, in some cases it may be desirable to inhibit the expression of endogenous PGD sequences in a host cell. Exemplary methods for practicing this aspect of the invention include, but are not limited to antisense suppression (Smith, et al.,1988); co-suppression (Napoli, et al.,1989); ribozymes (PCT Publication WO 97/10328); and combinations of sense and antisense (Waterhouse, et al., 1998). Methods for the suppression of endogenous sequences in a host cell typically employ the transcription or transcription and translation of at least a portion of the sequence to be suppressed. Such sequences may be homologous to coding as well as non-coding regions of the endogenous sequence. In some cases, it may be desirable to inhibit expression of the PGD nucleotide sequence. This may be accomplished using procedures generally employed by those of skill in the art together with the PGD nucleotide sequence provided herein.
Standard molecular and genetic tests may be performed to analyze the association between a cloned gene and an observed phenotype. A number of other techniques that are useful for determining (predicting or confirming) the function of a gene or gene product in plants are described below.
DNA taken form a mutant plant may be sequenced to identify the mutation at the nucleotide level. The mutant phenotype may be rescued by overexpressing the wild type (WT) gene. The stage- and tissue-specific gene expression patterns in mutant vs. WT lines, for instance, by in situ hybridization, may be determined. Analysis of the methylation status of the gene, especially flanking regulatory regions, may be performed. Other suitable techniques include overexpression, ectopic expression, expression in other plant species and gene knock-out (reverse genetics, targeted knock-out, viral induced gene silencing (VIGS, see Baulcombe D, 1999).
In a preferred application, microarray analysis, also known as expression profiling or transcript profiling, is used to simultaneously measure differences or induced changes in the expression of many different genes. Techniques for microarray analysis are well known in the art (Schena M et al., Science (1995) 270:467-470; Baldwin D et al., 1999; Dangond F, Physiol Genomics (2000) 2:53-58; van Hal NL et al., J Biotechnol (2000) 78:271-280; Richmond T and Somerville S, Curr Opin Plant Biol (2000) 3:108-116). Microarray analysis of individual tagged lines may be carried out, especially those from which genes have been isolated. Such analysis can identify other genes that are coordinately regulated as a consequence of the overexpression of the gene of interest, which may help to place an unknown gene in a particular pathway.
Analysis of gene products may include recombinant protein expression, antisera production, immunolocalization, biochemical assays for catalytic or other activity, analysis of phosphorylation status, and analysis of interaction with other proteins via yeast two-hybrid assays.
Pathway analysis may include placing a gene or gene product within a particular biochemical or signaling pathway based on its overexpression phenotype or by sequence homology with related genes. Alternatively, analysis may comprise genetic crosses with WT lines and other mutant lines (creating double mutants) to order the gene in a pathway, or determining the effect of a mutation on expression of downstream xe2x80x9creporterxe2x80x9d genes in a pathway.
Other analyses may be performed to determine or confirm the participation of the isolated gene and its product in a particular metabolic or signaling pathway, and to help determine gene function.
All publications, patents and patent applications are herein expressly incorporated by reference in their entirety.
While the invention has been described with reference to specific methods and embodiments, it will be appreciated that various modifications and changes may be made without departing from the invention.